2. Determine whether recurring subsets or patterns of SE SNPs can be identified that are causally linked to outbreak potential of other Salmonella serotypes, and determine if SNPs can be used for risk profiling and cluster detection.

3. Apply information about genomic variation occurring across Salmonella enterica to improve serotyping schemes and vaccines that can be used to develop rapid and sensitive diagnostic and epidemiological testing methodologies for SE in poultry flocks and eggs.

1b.Approach (from AD-416):
Sixteen genes have been identified that are disrupted by SNPS SNPs in strains that vary in virulence potential. These genes will be mutated in a parent strain with a characterized genome and will be assayed by phenotype microarray and hen infection studies for function in virulence pathways. New SNPs will be identified that differentiate prominent phage types that vary in geographical incidence using whole genome comparisons. SNPs that have been linked to virulence or geographical incidence will be analyzed across other Salmonella serotypes by primer-directed sequencing for the purpose of evaluating epidemiological trends associated with SNPs.

3.Progress Report:
ARS researchers in Athens, GA determined that the cost of serotyping Salmonella could by lowered by 80%. The serotypes were identified by a new molecular typing method developed at ARS and tested against a method that has been verified in Europe. Less expensive and simpler laboratory assays may help increase testing by industry and especially aid the ability of private companies to assess for the presence of more dangerous serotypes on-farm and in imported foods and food products without having to involve external entities.

ARS researchers at Athens, GA made a new vaccine for reducing persistence of Salmonella in the internal organs of hens. Two trials were done to test a new type of vaccine in hens. It appears that the protein of interest, namely sefD, may help protect against persistence of Salmonella in the organs of birds. Industry partners will be informed of results.

Subordinate project report completed work associated with NFCA Number 58-6612-9-164FN. Isolates and substantial scientific information on the background of isolates were previously submitted to this project and collaboration has ceased.

4.Accomplishments
1.
Intragenic Sequence Ribotyping (ISR) for serotyping Salmonella enterica helps international trade partners assess the safety of food. International trade partners have difficulty obtaining serotype for the major food borne pathogen Salmonella enterica at reasonable cost. ARS researchers at Athens, GA compared ISR to a certified DNA microarray method, and found ISR it to give comparable results at a fraction of the cost. The impact was that USDA was able to provide serotype information to major trade partners in Columbia, Brazil, Peru and Argentina, as well as to multi-national agriculture companies. The ISR method facilitates exchange of information about Salmonella serotypes across international boundaries, which protects the American consumer by enhancing the safety of the food supply.

2.
Biosensor technology robustly detects strains of Salmonella enterica that vary in outer membrane components. Preventing pathogens from spreading in the air, in water and in food supplies is facilitated by rapid methods of detection, and new approaches are needed to improve detection. A company that had developed an antibody-based biosensor approach needed more information on its ability to detect Salmonella enterica, which is known to have a cell surface that can vary greatly as targets for antibodies. USDA researchers in Athens, GA provided a set of 26 strains and mutants that would stringently test the ability of the biosensor technology to detect Salmonella enterica with variable cell surfaces. One strain was found that could trick the technology, but does not occur in nature. The lower limit of detection for the technology was somewhat strain dependent, but it still compared favorably with other methods such as the polymerase chain reaction. This research facilitates accurate application of a promising technology. The company sponsored presentation of the research at the International Association of Food Protection Annual Meeting.